Transcriptomics

Training material for all kinds of transcriptomics analysis.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Introduction

Start here if you are new to RNA-Seq analysis in Galaxy

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Transcriptomics
Reference-based RNA-Seq data analysis
De novo transcriptome reconstruction with RNA-Seq

End-to-End Analysis

These tutorials take you from raw sequencing reads to pathway analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
1: RNA-Seq reads to counts
2: RNA-seq counts to genes
3: RNA-seq genes to pathways

Visualisation

Tutorials covering data visualisation

Lesson Slides Hands-on Recordings Input dataset Workflows
RNA Seq Counts to Viz in R
Visualization of RNA-Seq results with CummeRbund
Visualization of RNA-Seq results with Volcano Plot
Visualization of RNA-Seq results with Volcano Plot in R
Visualization of RNA-Seq results with heatmap2
Pathway analysis with the MINERVA Platform

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
CLIP-Seq data analysis from pre-processing to motif detection
Differential abundance testing of small RNAs
GO Enrichment Analysis
Genome-wide alternative splicing analysis
Network analysis with Heinz
RNA-RNA interactome data analysis
RNA-Seq analysis with AskOmics Interactive Tool
RNA-seq Alignment with STAR
Small Non-coding RNA Clustering using BlockClust
Whole transcriptome analysis of Arabidopsis thaliana

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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Community Resources

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoBérénice Batut avatar Bérénice Batutorcid logoMaria Doyle avatar Maria Doyleorcid logoFlorian Heyl avatar Florian Heyl

Contributors

This material was contributed to by:

orcid logoMallory Freeberg avatar Mallory FreebergChao Zhang avatar Chao ZhangBelinda Phipson avatar Belinda Phipsonorcid logoMartin Čech avatar Martin ČechDaniel Maticzka avatar Daniel Maticzkaorcid logoMaria Doyle avatar Maria Doyleorcid logoBérénice Batut avatar Bérénice Batutorcid logoGraeme Tyson avatar Graeme Tysonorcid logoMira Kuntz avatar Mira KuntzShian Su avatar Shian SuJames Taylor avatar James Taylororcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoHelena Rasche avatar Helena Rascheorcid logoClemens Blank avatar Clemens BlankCharity Law avatar Charity LawNiall Beard avatar Niall Beardorcid logoToby Hodges avatar Toby HodgesMehmet Tekman avatar Mehmet Tekmanorcid logoMateo Boudet avatar Mateo BoudetMarius van den Beek avatar Marius van den BeekHarriet Dashnow avatar Harriet DashnowEkaterina Polkh avatar Ekaterina PolkhCasper de Visser avatar Casper de VisserSimon Bray avatar Simon Brayorcid logoTeresa Müller avatar Teresa Müllerorcid logoCristóbal Gallardo avatar Cristóbal GallardoAnton Nekrutenko avatar Anton Nekrutenkoorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamXavier Garnier avatar Xavier GarnierGildas Le Corguillé avatar Gildas Le Corguilléorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBjörn Grüning avatar Björn GrüningIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoClea Siguret avatar Clea SiguretPeter-Bram 't Hoen avatar Peter-Bram 't HoenJovana Maksimovic avatar Jovana Maksimovicorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzMatt Ritchie avatar Matt Ritchieorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoErwan Corre avatar Erwan CorreAnna Trigos avatar Anna Trigosorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoArmin Dadras avatar Armin Dadrasorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosAnne Siegel avatar Anne SiegelMarkus Wolfien avatar Markus WolfienOlivier Dameron avatar Olivier DameronAndrea Bagnacani avatar Andrea Bagnacaniorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoMo Heydarian avatar Mo Heydarianorcid logoLucille Delisle avatar Lucille DelisleCharlotte Adang avatar Charlotte AdangXi Liu avatar Xi Liuorcid logoFlorian Heyl avatar Florian Heylorcid logoLinelle Abueg avatar Linelle Abuegorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMatti Hoch avatar Matti Hochorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoAnne Fouilloux avatar Anne FouillouxWilliam Durand avatar William Durandorcid logoSofoklis Keisaris avatar Sofoklis KeisarisJosé Manuel Domínguez avatar José Manuel DomínguezMateusz Kuzak avatar Mateusz Kuzakorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijk

Funding

These individuals or organisations provided funding support for the development of this resource

References